Fly Off-Peak - You are more likely to have an open seat next to you.
Avoid Long Layovers - I always travel SAA. I love the leg room, the TV and all the snacks my son could ever want or possibly need! I also love the fact that they have a direct flight from JHB to Cape Town. The downfall is Cape Town is two hours away, but I would much rather have a little extra drive time then have to switch planes.
Check Stroller At Gate - This kind of seems like a no brainer, but some people don't do it. It's so nice having a stroller waiting for me as I exit the plane, instead of having to carry my son to baggage claim.
Be Prepared To Entertain - If you have your heart set on napping you may be disappointed. I've found if I'm mentally prepared to entertain my son for the first two hours he is more likely to fall asleep soundly for the final two. It's those flights where I'm hoping to can relax that turn into a nightmare.
Dress In Easily Removable Layers - Airplanes can get hot then cold and then hot again. So make sure you either dress your child in layers, or that you have a sweater near by. I also prefer to dress him in an outfit that I can change a diaper in quickly if I need to.
Change of Clothes - You never know when your child is going to hit the tray while his milk and your Sprite are sitting on it. Opened. That happened. Sprite everywhere...including my new shoes I had never worn before. At least it wasn't Coca Cola, right? Luckily I had a spare shirt and pants for him to change into.
Headphones - Get your child some headphones so they can play a game or watch a movie. They have infant head phones. We found some that fit over his head. He does have a big head though.
Games/Movies - Buy a cheap portable DVD player, or take your iPad or iPhone with a DVD or two downloaded. Before we had our own iPad we were flying home and Ahnree was begin very fussy and nothing we did consoled him! Luckily we just happened to be on a flight with one of my husband's old friends from high school and he let us borrow his iPad. Life Saver!
Portable Mobile Charter - My husband got one at a conference, I haven't had to use it yet but it says it keeps charging for up to two hours. All you do is plug it into your phone or iPad and you're set. No cord or electricity needed. Just make sure you charge it before hand of course.